A Question Through Time
by Signs of Dusk
Summary: He had thought he could out run anything. He had thought that by running he could save himself from his sins. But he couldn't run forever. Someone wishes him dead, and the Doctor must meet his fate if he is to protect all that he holds dear. If he is to set things right, the present must uncover the past to save the future.
1. Prologue

**A/N: I do not own Doctor Who**

Prologue

The sound of laughter tinged with hysteria carried through the still atmosphere and traveled down a hall of prison cells, broaching near cynical with its mocking bite towards the end as it tapered off.

"Come on!" the voice taunted. "I know you can do better than that!"

The person's words were replaced too quickly with screaming that lasted no more than a minute before cutting off abruptly. The silence that followed, in the opinion of one of the cells' occupants, was immensely more painful to hear. At least then they knew that her fellow prisoner was currently alive.

She counted the seconds off in her head until the charismatic laughter returned. A hundred and eleven. A lot longer than it typically should've taken for him to be revived. She wondered what could've been done to him this time.

Clutching at the bars of her prison door, she pressed her face up against the tiny window and watched as the door across from her off to the right opened. Two men stepped out, hardly sending a glance her way as they travelled down the hall and disappeared around the corner.

She waited until she was sure they were long gone before daring to speak. "Hey . . ." she called. "You alright in there?"

Her inquiry was met with a mild chuckle. "Right as rain, sweetheart. Takes more than a couple thousand volts to do in ol' Jack Harkness."

"Good to know then . . ." she sighed, pulling away from the door to turn back to her bed. Sinking down upon the mattress, the young woman leaned her elbows upon her knees and stared at the cold floor, lost in despairing thoughts.

Just how long had she had been here? She glanced briefly to her left at the stone wall, taking in the numerous tally marks that had been chalked into the masonry. There were too many to count and she had soon given up the pointless endeavor of marking the passage of time she couldn't properly measure ages ago. Not when she hasn't seen the light of day in forever.

It sure felt like forever, and even now she began to question the likelihood of ever being rescued. And the longer she remained imprisoned in heaven-knows-where, the more her faith in a so called man with many secrets and a dozen faces began to dwindle.

Surely he should've been here by now?

"You wouldn't happen to know if they brought her back yet, would you?" asked Jack in a voice marred with reserved hope.

She shook her head in spite of the fact that there was no way that he'd even see the gesture. "Not yet. But I'd expect she'd be back soon enough. They never keep her for more than day if I'm figuring this out correctly." She glanced around thoughtfully before admitting, "Though I could be wrong."

The door down the hall opened suddenly, grabbing their attention. She immediately rushed back to her door, peering out into the dim light to watch as the two guards that had been torturing Jack returned with a disheveled brunette between them. The two men dragged the unconscious woman all the way to the furthest cellblock, their movements taken in ravenously by both her and Jack.

Their eyes met from across the way as the guards and their prisoner disappeared from sight. A mutual understanding passed between them as they stared into one another's eyes. An understanding that they could no longer wait for the off chance that they were all rescued; that was merely a pipedream at this point.

A plan for all of them to escape was downright foolish, and one that would never succeed. But if one of them . . . if one of them could escape, then that one person could give a message, to the man that Jack spoke so fondly of. The man with many secrets and a dozen faces.

A message to a man called the Doctor.

* * *

_Author's Note: This was originally going to be a lot longer, but I was so indecisive over the final version of it that, for the sake of remaining vague, I ended up with what you see here. _

_Everything will be explained in time, trust me. And dozens of familiar faces will make an appearance, some more than others. Hopefully you all will be pleased._

_And, just to warn you, things may seem chaotic for a while, 'cause there'll be multiple timelines going on at once, (timey wimey and all) but rest assured that everything will be sorted out by the end._

_Next chapter: Of Fire And Ice_


	2. Of Fire And Ice

**A/N: I do not own Doctor Who.**

Ch. 1

The Doctor rushed through the dilapidated remains of his tomb, trying his best not to jostle Clara too much as he carried her in his arms. The others struggled to keep up with his mad sprint, all slightly perturbed to varying extents at the Doctor's rather frantic behavior.

"Come now, you all!" he called out. "Keep up will yah!"

"Sir, if I may, what is the nature of this retreat?" inquired Strax. "If we are under enemy attack then might I suggest we turn around and face it in glorious battle?"

"This isn't the sort of thing that can be fought!" the Doctor yelled, unable to hide how exasperated he was for the Sontaran's continuous desire to implement violence as a means of resolving issues. If only it were that simple. "Besides, I never said we were running from someone."

"No, but you are running from _something_." Madame Vastra remarked in slight challenge, daring him to refute the obvious.

He kept quiet, ignoring the point of contention that the Silurian was attempting to make. It wasn't his place to drag them into this any further than he already had, and as it were, having just one person aware of one of his more deeper, darker, secrets was frankly one person too many.

Nothing more was said between the motley crew as they traversed through the bowels of what was to be the Doctor's ship. Eventually, through the ceaseless demands that they keep moving by the Doctor, they were able to make it out of the tomb in relatively good time and back to the proper TARDIS.

The Doctor only slowed long enough to settle Clara against one of the walls for the others to attend to her. After that, he was a flurry of movement, hastily moving around the console to various dials, buttons, and levers in an attempt to coax his obstinate ship back to life.

It took quite a bit of convincing on his part, but eventually she awoke and hastened their departure, eager to be rid of the crisscrossing timelines scattered all around them. He couldn't agree with her more, though for reasons far more personal than that of the laws typically governing time-travellers.

It wasn't until the TARDIS was well on its way from Trenzalore that the Doctor allowed himself a moment of pause. He slumped heavily against the console, letting out a slow breath as he was finally able to relax.

"Doctor," called Madame Vastra softly as she strode to his side. "What is it that you saw while you were in your own timeline? Now, don't you go denying it. I know when something is bothering you."

The Doctor gave her a sidelong glance, looking his age despite his deceptively youthful visage with the ancient smolder in his eyes. A small, enigmatic smile filled with dark amusement played at his lips as he answered, "I saw the past, of course. Blasts from the past as it were. A long history I have, you know. Was able to get reacquainted with a few familiar faces."

Madame Vastra held her tongue, refusing to rise to the subtle bait he was presenting to her. She knew he was merely dancing around the question, and for now she would let it slide. But only for now.

"It's nothing you should concern yourself with, Vastra," the Doctor asserted. "Trust me."

But looking at him now, while his eyes hinted to a soul of fire and ice, it was in these rare moments that she was reminded that she could not.

* * *

The Doctor sat in Clara's room, deep in thought.

He had arrived at the Maitland home after having dropped off Vastra, Jenny, and Strax to their proper time. It didn't surprise him to find that no one was home, giving him some relief that he could be alone for a while. Or, rather, as long as Clara slept, which promised him a couple hours at best.

He tucked her into her bed after setting aside the leaf that she had been clutching up until now, placed a glass of water at her nightstand, and held vigil in a nearby chair. While he watched her sleep, he pondered recent events and wondered how much Clara would remember about it all.

It would be ideal that she not remember any of it, but he knew that the odds of that happening were slim. She was his Impossible Girl after all; she had a natural knack of defying the odds.

No, she was bound to remember something of the ordeal. He just hoped that it wasn't . . . _him_. That black stain in his long history that he had kept buried for so long. He had long since deceived himself into believing that it hadn't happened. The face that wasn't the Doctor by name, his actions only justifiable through mere assurance that he had done the right thing. That in order to save, he had to destroy. Something that defied the moniker he had sworn to uphold.

Those had been dark times, both for him and his people.

For a while there, he had feared that, somehow, _he_ would follow him out of his own timeline. He had feared it ever since their departure. But being here, in the 21st century, alleviated some of the unprecedented anxiety. Still, he worried—needlessly perhaps—that somehow the consequences of his past misdeeds would catch up to him if he, for one moment, stopped.

It was absurd though, wasn't it? In all of his many years since the war, he'd yet to face any kind of retribution for his heinous though begrudgingly necessary actions. Maybe he never would. Maybe his guilt was punishment enough. Maybe it had merely been an incongruent set of coincidences that they had stumbled upon his buried identity.

But then . . . that would mean he actually believed in coincidences. And he, for one, did not.

They had come across _him_ for a reason, so what was it?

He pondered this for hours until Clara finally began to stir. He perked up at the sight of her brow scrunching forward slightly as she took in a deep breath, her eyes slowly opening.

"Doctor . . ." Clara breathed, voice hoarse with disuse.

He sprang forward at her call, immediately taking the glass of water and bringing the lip to her mouth. He tipped the glass back slowly, stopping only when she turned her head away. Setting it back on the nightstand, he took her hand in his own and gave it a firm squeeze.

"Don't you ever do something like that again," he chastised half-heartedly, dismay crinkling his brow.

Clara gave a weak yet sly smile. "It worked, didn't it?"

The Doctor leaned back and folded his arms against his chest, giving a dissatisfied huff. But he otherwise didn't refute her, which caused her smile to blossom further.

"Are you alright?" the Doctor asked when his displeasure had subsided. "How are you feeling?"

"Like I've just been split into countless copies of myself." She drew the duvet aside and sat up, her previous smile slipping away as she took on a much more thoughtful expression. "Doctor . . . who was that man back there? The one I've never seen before."

He glanced away, crossing his legs and clasping his hands over his top knee. For a moment he remained silent, leaving Clara to watch as he searched for some vague answer to feed her. An answer that wouldn't leave her satisfied, thereby forcing her to question him just as she always did until he cracked and spilled the truth.

But, to her astonishment, this wasn't another of those times.

The Doctor looked back to her, mouth set in a grim line and brow furrowed in thought.

"You were right, Clara. Secrets may make us feel secure, but they do not necessarily keep us safe." He gave a drawn out sigh that conveyed a deep weariness. "He is a part of me that I do not like to acknowledge, a part of me that I had banished to the back of my mind because the thought of it alone was just too painful."

"And what does that mean exactly?" asked Clara, still not quite getting it.

He gave another sigh, closing his eyes. A pained expression contorted his face as he reminisced. "I'm sure you're aware from your snooping that there was once a war, a terrible war, which was called the Last Great Time War."

She gave a reluctant nod, recalling the time she had once forgotten of when she had wandered into the library and read a bit from a large book that had been placed on display. But could he really blame her for being curious? The book had been asking to be read with its elegant binding and enticing title.

"Then you should know that I was instrumental in putting an end to it. But in order to do that, I had been forced to time-lock my entire planet to prevent the destruction of all of creation. And, naturally, they tried to stop me." His pained expression grew to one of torment once he opened his eyes, revealing fresh tears.

Clara stared, wide-eyed and sympathetic. As much as she would like to let the matter drop, now was the opportune moment to learn more about him and his mysterious past. Such a chance would likely never present itself again.

And maybe it would be cathartic if he finally came clean and admitted aloud what he had done that plied him with such guilt.

"What did you do, Doctor?" she asked softly, watching him patiently.

He fidgeted anxiously, covering his mouth with his hand as he avoided further eye contact. "Please don't make me say it . . ." he moaned miserably.

"Doctor . . ." prompted Clara gently.

He scrubbed a hand over his face roughly and abruptly stood. A look of anguish mixed with infuriation flashed across his youthful face until it finally settled to somber resignation.

"I killed whomever stood in my way," he grated out before spinning on his heel and retreating away.

Clara didn't have the heart to follow after him.

* * *

The weather was a complete dismal, reflecting perfectly upon his current mood. For a while he sat there, in the rain, uncaring that he was already chilled to the bone. He looked up at the night sky, choked with its many storm clouds, and longed for the sight of stars. Stars that told him that there were limitless worlds out there, all teeming with various forms of life. Life that was capable of choosing what was right or wrong. Good or bad.

Embittered, the man got up from the wet bench he found himself on and trudged along the empty streets to the nearby pub he had recently become familiar with.

A few people glanced up at him upon entering, but most hardly paid him much mind as he shrugged off his drenched duster and moved to his usual table in the corner. He draped the black coat upon a chair back carefully and sank down into the chair that kept his back turned to the wall, allowing him full view of the pub and its occupants.

Within moments the waitress working that night brought him his usual drink and he nursed it slowly, ruminating on his shortcomings. He often did this after a long day of still coming back empty handed, musing upon his failures and pondering possible outcomes if he had only done things differently. The what ifs and could-have-beens. All the while inevitably drinking himself into a drunken stupor that would most likely have him passing out in some alleyway on the way back to his place. It had happened to him three times already.

The man swiped a hand through his grey streaked hair, freeing droplets of water to splatter themselves across the greasy tabletop. After draining the last of his spirit in a final swing, he began to wonder just how often he came to this pub as the waitress placed another glass of his drink of choice in front of him. Often enough, it would seem, if the wordless gesture was of any indication.

His gloved hand moved to momentarily rub at his beard before he leaned his chin upon his rough palm. His bloodshot eyes invariably drifted to his left hand pressed flatly upon the sticky surface. He stared at the gold wedding band that he wore and subtly twisted his finger around to admire the way the metal caught the muted lighting in the crowded establishment.

A slight smile ghosted across his lips as he remembered the day that they had been wedded, and how happy they both had been.

Life had been happy back then. Simple, but very happy.

Now it was just Hell.

The subtle clearing of a person's throat caused the man to snap out of his short-lived reverie and he pointedly narrowed his eyes as he glared at the younger man who had had the audacity to approach him. No one had dared approach him before now, not in the few months he's been stuck here in this lonely city with its misleading clues.

"Um. . ." the man hesitated, a bit put off by the hostility being directed towards him. "Mind if I have a seat?"

"Yes," he bit out through clenched teeth, trying his best to remain civil in spite of his dwindling patience. "Now sod off."

The man ignored his command and seated himself across from him, periodically glancing over his shoulder at someone sitting at the bar for some kind of reassurance. Tension continued to build the longer the silence was left to carry on, marked by how uncomfortable his guest appeared to be the longer he was met with an unimpressed scowl.

"I said sod off, you bloody twit," he growled.

Instead, the anxious man slid over a folded napkin to him, swallowing nervously. "I was told to give this to you."

Unable to deny his curiosity, he momentarily dropped his glare to the napkin and debated on whether or not to pick it up. After all, it could be a clue. Or a poor prank. Either way, there was no way of knowing the napkin's contents unless he looked for himself.

With a reluctant hand he procured the napkin, opening it slowly to peer inside. His squinted gaze gradually widened as he took in the simple message.

"No. . ." he breathed in disbelief, snarling at the words that seemed to always follow him no matter what he did.

"Do you know what it me—" The younger man's words were cut off abruptly when he was yanked out of his chair and his back was slammed against the wall.

He held up the younger gentleman by his waistcoat, teeth bore in a feral snarl. "Who gave this note to you, huh? Who put you up to this?"

"She said you knew her!" he insisted. "Told me you both go way back."

Before the man could answer, the bell over the door chimed, drawing his gaze over to watch a blur slip away. It took a moment to process what he'd seen, to digest the quick flash of a woman walking briskly out of the pub.

He rushed wildly after her, having half a mind to leave a handful of bills and grab his coat before he had completely left the table. It was pouring even harder now, and it was a struggle just to see a few feet ahead of him. Looking to and fro for any signs of this mysterious woman that knew him, he was forced to pick a gamble and chose to turn left down the street, hoping he had chosen correctly. He'd hate to lose her off of a poorly made guess.

He became so focused on the task at hand that he was hardly paying any attention to the traffic in the street. And as he darted along a crosswalk, a car horn blared in warning, causing him to reactively stop to face the sound.

His eyes grew wide as the headlights broke through the foggy weather and landed upon him. The driver attempted to stop, slamming their foot upon the brake pedal, but the water drenched roadway made it nearly impossible.

There was no time to move, to duck, or roll, or even say a prayer.

The car was upon him in seconds and he was soon soaring.

* * *

_Author's Note: Let me know what you think. And feel free to speculate as to who that was in the second half of the chapter by leaving a review! Or not. Whatever floats your boat. Updates will be made on Wednesdays baring any unforeseen obstacle that may prevent me from doing so._

_Next chapter: Room Of Reflection_


	3. Room Of Reflection

**A/N: I do not own Doctor Who**

Ch. 2

After his admittance to Clara, the Doctor had stormed back to the TARDIS, desiring to be anywhere but back in that house where he had spoken aloud his crimes. He was slightly surprised that Clara hadn't raced after him like he expected she would—like any of his previous companions would've—but he was glad that she was giving him space. And frankly he didn't think he'd have the courage to face her after what he had said.

Inside the TARDIS, he wandered through passageways he hadn't traversed in decades, desiring solitude. His beloved ship was aware of this, retreating to a secluded corner of his mind to leave him be. He appreciated this immensely, for he didn't deserve any sort of comforting at the moment.

Eventually, partly because he didn't have a clue as to where he was going, he stumbled upon a room he had never visited before (which was a quite pleasant surprise because he had figured he knew every nook and cranny of the old girl). The corridor was walled all around with mirrors, lit by panels in the floor that diffused harsh light and casted sharp shadows everywhere.

The Doctor traversed the length of the hallway warily, glancing periodically to the sides when he thought his reflection wasn't his own. For the most part, this assumption was unprecedented until the hallway opened up to circular room with an antique armchair sitting at the center. All around were mirrors, mirrors that each held the figure of a past regeneration in place of his proper reflection.

He looked around in quiet awe, taking in the faces of his previous incarnations. But that sense of awe was quickly abated when his eyes fell upon _his_ dreaded face.

_He_ was standing there with his somber expression beseeching forgiveness upon his weathered face in between his eighth and ninth incarnations, both of whom appeared decidedly uncomfortable standing next to the man who had forsaken their sworn moniker.

"What are you doing here?" growled the Doctor, glaring at the pariah.

The man didn't reply. Knowing he was unwanted, he merely bowed his head, turned, and walked away. As he retreated, the light under the mirror seemed to dim until the glass was opaque with shadows so that nothing could be seen through.

For some time the Doctor stared at the tinted mirror, suddenly feeling his age. He ran a weary hand down his face as he sank into the armchair, becoming slightly amused when all of the other versions of himself simultaneously sat down as well.

"What is this place?" he asked aloud.

His chair turned suddenly, directing him over to his pinstripe suit wearing predecessor. The slightly older looking man gave a crooked grin, relishing the attention. "You're in the Room of Reflection. It allows you to converse with constructed data of your previous selves created by our time in the TARDIS that have been archived within the mainframe. Clever thing, really, I'm surprise we never discovered this room sooner. It sure beats having to sift through memories, let me tell you."

"Shut your trap, you incessant, big haired fool!" one of them shouted, earning a look of offense from his predecessor when some of them laughed at the sharp remark.

The Doctor smiled at the antics that the echoes of himself were gradually getting into as they began to squabble amongst themselves. As much as he'd rather just sit there and watch them bicker back and forth with each other, he had more pressing issues that he wished to discuss. It would help to hear a different opinion, even if said opinion was essentially coming from himself.

"I'd like to speak with those with the knowledge of the Last Great Time War."

Immediately the atmosphere grew thick with suppress tension and stress. His first seven faces grew grim as they stepped away—his fifth body in particular looking distinctly unsettled—until all that remained were three figures. His chair turned so that he could face them all at once. Despite their various postures, a clear sense of dread exuded from them all.

"What is that you wish to discuss?" asked the Eighth Doctor, leaning his chin further upon his knuckles.

"I have reason to believe that something is about to happen, if it hasn't already, something that has connections to what was done during the war," said the Doctor, hands tightening upon the armrests. "I saw . . . _him._ _He _approached me while I was in my timeline. I wouldn't think anything of it, but . . ."

"But it was the one who broke the promise," the Ninth Doctor finished, looking pensive.

"You do remember that little important bit about being the only survivor, right?" the Tenth Doctor reminded cheekily, struggling to lighten the mood. "No one has any record of what we did, excluding ourselves of course, let alone the war itself."

"True," the Doctor conceded, "and I did erase myself from all existing records."

"Then what's the problem?" asked the Tenth Doctor.

"The problem is that my actions have rippled throughout time," spoke a gravelly voice weighed heavily with despair.

The banished pariah returned without anyone's consent, infuriating the Doctor with his presumption and causing the others to shift around in their seats uncomfortably. The Ninth Doctor promptly stood and lumbered away when it became clear that his predecessor showed no signs of leaving, unable to take the sight of him any longer.

The Doctor tried to do the same, but was stopped by his dark shadow.

"There you go, running away again," he remarked in a tone tinged with disapproval. "Do you really think that you'll be able to flee from this forever?"

"Well I can damn well try!" snarled the Doctor, coming nose to nose with the abhorred reflection of his past.

"The past is resonating into your future, Doctor. Your sins haven't been forgiven yet, I'm afraid. You'd best prepare yourself for the storm that's approaching."

"What storm?" he grated out between clenched teeth, barely having the patience to remain civil. "What do you know?"

"Have you looked yourself in the mirror lately?" the man posed, his words becoming the final straw.

With a frustrated roar the Doctor struck the mirror repeatedly with a clenched fist, relishing at the resounding crackle of splintering glass. The reflection of the haunted old man desiring forgiveness distorted awkwardly along the spider web of cracks until the glass finally gave way and shattered into various sized shards that fell to the floor.

He stepped away and shook his hand, dispelling most of the glass with the exception of a few pieces that were piercing into his knuckles. He extracted the pieces carefully, wincing at the sharp pain that came with their removal. Once he was finished, he moved back to the chair and sank down into the plush cushion seat with a long-suffering sigh.

The Doctor sat there, hiding his face behind his uninjured hand, in silence.

* * *

Clara had half expected to hear the distinct whirl of sound the TARDIS made with every departure, but was surprised when such a sound never occurred. She looked out her window just to make sure she hadn't mistakenly missed it, but there it was, sitting innocuously on the street corner with no one the wiser.

Comforted by the fact that it didn't appear he was about to swan off anytime soon, Clara took her time cleaning up the house before the Maitland family returned. The house, already in relative good order, didn't take very long to tidy up. Once the dishes were washed and left to dry, and a sufficient enough time had passed for the Doctor to sulk, she decided to venture out in search of the man.

In her many adventures she'd had with the Doctor, Clara could reasonably say that the TARDIS and her didn't quite see eye-to-eye. Putting aside her still skeptical belief that this old police-box was nothing more than a ship, she did believe that it was trying to divert her from her search for the Doctor.

She traversed down several hallways—too many hallways in her opinion—and passed several rooms. Most of the doors were unlocked, giving Clara the clearance to have a quick peek inside and see if he was there.

So far the music room, the cloister room, the kitchen, the gardens, the sun room, and the art gallery were out of question. And he didn't appear to be in the library, much to her consternation. If he was to be anywhere, she'd think it would be there but apparently she was misguided for assuming so.

"Come on . . ." Clara said aloud, glancing nervously at the walls. "I just want to make sure he's alright, is all."

The overhanging lights pulsed and a dull hum rang in the back of her mind, providing her a sense of reluctant allowance. The hallway darkened and the right corner at the end of the hall suddenly lit up with a path for her to follow. Voicing a quick thanks, Clara ventured onward with renewed vigor, putting faith that the TARDIS would not lead her astray.

However, she began to have her doubts when she ended up down a corridor of doors with name plaques she'd never seen before. A hush silence fell all around and it felt very much like she was intruding on something that was better left alone. But, never one to ignore her own curiosity, Clara continued on with a growing sense of intrigue.

She opened the first door on her left—this one belonged to a Susan—and was greeted with the sight of a well-kept though sparse bedroom that didn't appear to have been occupied in the longest time. She closed the door carefully and moved on to the next, the plaque having the name Adric written on it. In it was another bedroom, this one filled with several astronomy books and a large whiteboard with a lengthy equation left unsolved.

It didn't take long or even much investigation for her to come to the conclusion that the corridor was filled with rooms once belonging to previous companions, all perfectly preserved. The only thing particularly alarming was the number of rooms that lined the lengthy corridor. Just how many people had the Doctor travelled with in all his years? And, more importantly, what had happened to them all?

A chill ran down her spine and Clara gave an involuntary shiver before continuing onward. She walked to the very end where the paint on the doors didn't appear quite as faded, passing names like Sarah-Jane, Romana, Tegan, Ace, Jack, Martha, and Donna. She peeked inside the last one on the right, denoted with the word Ponds, taking in the king-sized bed freshly made, the dresser covered in toys that looked bizarrely like the Doctor and the TARDIS, and the framed photos that sat on the two nightstands. She took particular interest in the one with the wedding photo, noting how happy the couple looked.

"What are you doing?"

The unexpected inquiry and sudden placement of a hand on her shoulder had Clara jumping quite skittishly, spinning on her heel quickly to come face to face with the Doctor's puzzled expression.

"Looking for you, you big lump!" she exclaimed, pitch slightly strained from her prior alarm. "I was starting to worry when the TARDIS was just sitting there."

"Needlessly, I assure you," the Doctor waved aside. He glanced over her shoulder and his demeanor grew cold. "Come on, there's no need to be here in this old place." Before she could protest the Doctor took her hand and began leading her away.

She pretended not to notice the stained scrap of cloth wrapped around the palm of the hand holding tightly onto hers. Instead of questioning him about it she decided to ask him something else. "What exactly is this place?"

The Doctor gave a fond smile as he glanced at the passing doors, a wave of nostalgia crashing into him as various memories sprang to the surface of his mind. "This, this is where I keep all the rooms of my previous companions. All of them, kept exactly the way they were the day their occupant or occupants departed. Well . . . nearly. I had a bit of a run-in awhile back with an entity that had deleted all the rooms. But I, I made sure they were all properly restored."

"You've sure have had a lot of them," Clara pointed out, not because she was jealous but because she was merely curious. The Doctor wasn't always particularly forthcoming when it came to personal information.

"Yes, well, after hundreds of years and several different faces, you do tend to get lonely every once in a while. And it's always nice to see the universe through a pair of fresh eyes, 'cause believe me, the novelty of having the whole of time and space washes away after the first hundred years of adventuring when you've seen it all."

"What happened to them, the others?"

"When it's time to go, it's time to go." The Doctor's eyes drifted to the only door that didn't bear a name. He stared at the stenciled flower on the wood before quickly looking back forward, swallowing passed the lump that had formed in his throat. "But they're all doing well as far as I know."

A jubilant smile suddenly broke across his face as he asked, "While you're here, how would you like it if we'd take a low-key trip somewhere? Anywhere you'd like. I think we'd both could use bit of vacation after all that's happened."

Clara could tell that he was trying to change the subject by distracting her with the prospect of vacation anywhere in time and space. But she kept such a thought to herself, knowing that he was likely still worked up by his earlier admittance.

"Sure," said Clara. "How 'bout a trip to a nice spa on some exotic planet that has no possibility of resulting in some sort of peril?"

He mulled it over with a slightly sour look, trying not to get too disappointed. "Well, I suppose if that's what you want. . ."

Clara laughed at his attempt of sounding enthusiastic. "I'm just kiddin'," she assured with a bemused smile. "I honestly don't care where we go, so long as it's an adventure."

The Doctor took a moment to study her, to marvel at his Impossible Girl, before a manic grin split across his face. "Off we go!" he exclaimed as he sprinted forward, tugging Clara along.

As he lead her through the labyrinth of hallways, it struck her that, in spite of the hardships that came with following a man like the Doctor, she wouldn't have her life any other way.

* * *

His shift at the hospital had just recently ended, a fact that he was steadily coming to regret. It was pouring outside, and he hadn't had the foreknowledge to even bring an umbrella. Coupled with the fact that his wife was the one with the car, it made for a rather dreadful trip to the flat.

All he could do was pop up the collar of his trench coat, keep his head low, and hope for the best. Not that there was much to hope for. Either way he was going home soaked.

He trudged through the awful weather, grumbling about his poor luck, and made it down a few blocks when he heard the squeal of rubber tires down the road. The harsh sound brought him to an automatic stop, his gaze moving away from the ground so that he could squint through the mist and try to discern the problem.

To his abject horror, he watched as a man was run downed by the vehicle in question, the unfortunate victim first hitting the front bumper and then the windshield. The man flailed through the air momentarily while he passed the top of the car until gravity took its eventual effect and he fell ruthlessly to the ground. But before the stranger could even hit the pavement he was rushing towards his aid, preparing for the worse yet hoping for the best.

He knelt down beside the broken man, removing his droplet covered glasses to get a better look. To his surprise the man was still conscious, although just barely.

"Sir," he called. "Sir, everything is going to be alright. Try to stay awake for me."

The man looked to him with pleading eyes, his shallow breaths quickening in a show of escalating panic while he began to whimper. His right hand shot out to take his wrist desperately, struggling to speak.

"Don't talk. Trust me, I'm a nurse," he advised, cringing at the impossible grip the victim had upon his wrist. It felt like iron with its steady application of pressure. He feared that if he kept it up, the man would end up snapping his wrist, as absurd as it seemed.

He took note of the sound of car doors opening and closing, signaling the approach of the driver and a few other pedestrians.

"Oh God," the driver breathed at the sight of the broken man lying in the road, taking in the awkward angle of his right leg and bloodied face. "I swear I . . . he just appeared out of nowhere!"

"Phone for an ambulance!" he roared over his shoulder, knowing time was of the essence. Looking back to the victim, he noted the way his crying eyes were starting to lose focus, showing the immediate signs of a concussion. Now he really needed to stay awake.

He covered the hand that was gripping his wrist with his free one, trying to convey the fact that this unfortunate stranger wasn't alone. "You've got to stay awake, you hear me? Help is on the way, just hold on."

In the midst of his gasps and sobs, the man sputtered an incomprehensible word. It took him a few seconds to notice this, and when he did, he leaned forward to spare the man the unnecessary effort.

"UNIT . . ." the man whispered, tightening his grip for emphasis.

He looked to him in puzzlement. The word sounded vaguely familiar, but he couldn't quite place where he had heard the term before. "I'm sorry?"

"UNIT . . ." he repeated. "Torchwood . . .?"

"I'm afraid I don't know what you mean, sir."

The man coughed a high and wheezing sound, spitting out pink saliva. "Doctor . . ." he sighed, his eyes slowly starting to close.

"Well, I'm actually a nurse, but just as well I suppose," he assured sheepishly. "Hey, what did I tell you about staying awake? Come on now, just a little bit longer, I promise. The ambulance should be here soon, seeing as how we're not too far from the hospital."

"Can't . . . let them . . ." the man gasped, fighting to remain conscious. "H-Hand . . ."

He felt the hold on his wrist instantly slacken, allowing all the blood to rush down in his numb hand and bring feeling back to his fingers. The man offered his hand up, silently beckoning him to remove the worn leather glove. He did so reluctantly, afraid of what he might find.

As the wail of sirens grew louder and louder in the cold, wet night, he looked down with mild astonishment at the man's hand, surprised to find a robotic appendage in its place that had once appeared deceptively human underneath the glove.

All he could do was balk at the exposed wires and turning cogs not concealed by the patches of metal plates as it steadily occurred to him that this man was apparently not of this time. Or perhaps even this world.

In spite of his reservations towards this unexpected reveal, he clasped the man's mechanical hand as if he harbored no qualms, noting the subtle relief flood the man's exhausted eyes.

"I understand that you're not from around here," he stated knowingly. "But that's ok. Neither am I."

* * *

Her feet hit the ground running.

It didn't matter where she was going or where she had been. Her only objective was to get away. To get away from them and the awful hold they had once had on her.

In all her years of adventuring, of finding herself in the middle of rather hairy situations, she'd like to believe that she was fearless. She had faced many a foe with a confidant smile on her face, seen things that would make lesser people break. She might as well laugh in the face of danger because there was hardly anything in the whole of creation that scared her.

But they . . . they made her fear. Even after all this time.

Racing down the empty London streets, she kept to the shadows, hoping it would lend her some cover in her quest to shake off her pursuers. She was just passing a street corner when she was unceremonious yanked into the dim alleyway.

The unexpected disruption had her fighting her capturer, able to deliver a solid right hook before she was pinned against the wall.

"Blimey, remind never to stumble across you in a dark alley a second time," the woman quipped, working her jaw slowly. While she hissed in pain, the other woman eyed her incredulously through the darkness, slightly baffled and mildly impressed that she had been accosted by a woman rather than a man.

A strange sense of familiarity struck her as she studied her capturer—savior?—only able to note her dark skin and clothing that made it easy for her slip into the shadows if need be.

"Who are you?" she asked with the curious tilt of her head.

"Name's Martha Jones. Now, d'ya mind tellin' me why those blokes in the uniforms are after you?"

The name ignited a spark of recognition in her and she couldn't help but chuckle lowly at the irony. She wasn't quite as afraid now that she wasn't alone. What were the chances that she'd run into one of the Doctor's past companions? Not many, that's for sure.

There was a reason, a purpose, that they'd meet in this off-chance manor. And the prospect of figuring that reason out delighted her endlessly.

"What's so funny?" questioned Martha, slightly annoyed by the other woman's sudden outburst of laughter.

Instead of answering Martha's inquiry, she offered her a hand. "Professor River Song, archaeologist."

Martha took the proffered hand warily, puzzled by River's sly smirk.

"The reason why I laugh is because I believe we were destined to meet. But I'll explain that later," assured River. "Now I think its best that we run."

* * *

_Author's Note: Some more surprises next chapter! Thank you everyone who reviewed/favorite/follow this story!_

_Next chapter: The Matter At Hand_


	4. The Matter At Hand

**A/N: I don't own Doctor Who**

Ch. 3

He was looking over John Doe's charts when the doors down the hall were pushed open with a flourish.

"This better be important, Rory, because I was in the middle of a major breakthrough with my story," said a testy Scottish redhead who eyed the man with the slightest traces of annoyance.

Without moving the eyes away from the clipboard he had in one hand, he used the other to pull out the mechanical appendage from his coat pocket to wordlessly show his wife. This got her to settle, her prior vexation disappearing.

"What's that?" she asked, staring disbelieving at the complex piece of machinery.

"It belongs to a man who was hit by an automobile an hour ago. He's in surgery now for a dislocated hip, shattered pelvis, and broken leg." Rory's eyes flicked over to the robotic hand. "I was on scene with him when it happened. He removed it before the ambulance arrived, making me promise not to breathe a word."

The redhead moved to stand beside her husband, peering down at the hand. "Who d'ya reckon he is?"

"I don't know," admitted Rory. "But that's not why I called you, Amy." He returned the hand back into his jacket pocket and pulled out a cylindrical object that looked like some kind of tool or device with its various settings and blue-tinted glass tip.

Amy's eyes widened further as she took the object into her hands.

"Please tell me I'm not the only one who thinks this looks like what I think it looks like." Rory said carefully, not wanting to be wrong but a piece of him hoping he wasn't right. Even after several years of living together in 1940s New York, he still had his insecurities towards a glorified phantom. And this man, whoever he was, wasn't helping things.

"If you're thinking that that looks like a sonic screwdriver, then yeah, I'm thinking that too."

* * *

Rory and his wife Amy frequented the waiting room while they waited for the stranger to emerge from surgery, neither of them knowing exactly why it was they were doing there but knowing that they'd never be able to rest until they found out who the man was.

Although they both felt like they knew. It was only a matter of being proven correct.

"You s'pose it's him?" Amy remarked quietly, fiddling with the hem of her blouse, looking at everything but her husband.

He gave a sigh as he took her hand—partly out of impulse and partly because he wanted to still her nervous gesture—and rubbed her knuckles soothingly with his thumb. "Let's not get our hopes up. For all we know it could be just coincidence."

Amy gave him a skeptical look. "Since when has anything pertaining to the Doctor been just coincidence?"

"We don't know that!" Rory began, his protestation ending short when he noticed one of his colleagues approach him, a nurse that typically took the shift right after his.

He didn't know her very well personally, but she had to be of good character if she was coming over to him to let them know about the man whose identity remained to be seen. As of now, after hours of constantly inquiring about the status of the patient, nobody had been willing to divulge any information to him.

"How is he?" asked Rory as he and Amy stood, involuntarily squeezing her hand.

The nurse glanced warily over her shoulder before turning back to the couple, a troubled look crinkling up her brow. "They're taking him out of surgery now, to one of the private rooms. But, I have to tell you, it's a good thing that he came in when he did. He's a very sick man."

Rory felt Amy clutch at his hand tighter, her concern mirroring his own. Stranger or not, it was still a cause to be worried.

"Thank you, Olivia, but why are you telling me this? After all, we're not the next of kin, so you're going against protocol by informing me about the situation."

"Well, nobody knows who he is. And from the state you found him in, I'd guess he doesn't have much of a family. A man in his position deserves to have someone worry about him," Olivia stated before a bemused smile lifted the gloom from her round features. "Besides, we all know you won't quit hounding us about him until you finally get your answers. But you didn't hear it from me."

He smiled appreciatively at his coworker as she moved away from them, likely to prepare the room in which the mysterious man was to be placed in. He took special care of discreetly watching where she went before turning back to Amy, gazing sympathetically at her worry.

"Hey, it's going to be alright," he soothed, struggling to remain hopeful in spite of it all.

Amy couldn't respond, not without revealing how certain she was that it was _him_.

And if she was right, then something was terribly wrong.

* * *

Waiting another hour to make sure no one would notice if they were to enter a patient's room well past visiting hours, the couple discreetly slinked into the room housing the man, mindful to remain quiet.

Rory took note of the equipment that the man was hooked up to, nodding his approval while Amy stepped forward and studied his face.

He looked older, much older than they were with prominent lines around his eyes from much laughter and across his forehead from much thought and grey streaked brown hair that shimmered silver in the light. His brow was furrowed and his mouth was set in a ghost of a scowl. It seemed that, even in sleep, he could not retrieve respite. She wondered what demon plagued him so heavily this time.

Amy and Rory each took a chair and brought it close to his bedside before sinking down to continue their unexpected vigil.

Neither knew exactly how long they sat there, trying to distract themselves from what laid blatantly in front of their eyes, until the mysterious man finally began to stir.

It was Amy who noticed first, sucking in a quiet gasp that went unnoticed by her husband sitting opposite of her. "Rory," she called, snagging his attention. He looked up and sat up a little straighter when he noticed the man's eyes start to flutter open.

John Doe gave a low groan as he slowly opened his eyes, blinking repeatedly to clear away the film that obscured his vision. Once he could see again, he lethargically took notice of both his surroundings and the couple hovering at his bedside, becoming instantly confused.

"Where am I?" he croaked hoarsely. "What happened?"

"You were hit by a car last night," answered Rory, gazing at him sympathetically. "You ended up breaking your leg and pelvis and dislocating your hip. Consider yourself lucky though, 'cause it could've been a lot worse."

The man scoffed disdainfully and made to sit up when he paused suddenly, his expression growing alarmed as he extracted his right arm from under the scratchy sheets.

He stared wide-eyed at the scarred stump, demands of what had happened to his hand already forming in his throat as he looked back to Rory, only to notice that the nurse was already presenting him with his mechanical appendage.

"I kept it safe, just as you asked." Rory said as the man snatched it from his grasp.

The couple watched in uncomfortable silence as he reattached the advance prosthetic back onto his arm, his face contorting to a painful grimace as all the barbs lining the opening of the wrist broke skin and latched onto the viable muscle nerves underneath. Reestablishing the connections for the electric pulses to pass seamlessly from his nerves to the wires was always uncomfortable, but his current state of health made it particularly unbearable and it was a fight not to make his pain known.

Biting back his cries of discomfort, he stared fixedly at his hand for several seconds until each mechanical digit slowly began to retract to a closed fist. He flexed his fingers and opened and closed his fist repeatedly until the motion was smooth and consistent, though the simple effort continued to pain him.

Amy and Rory noticed how haggard and drained the man was after reattaching his prosthetic, but he didn't appear to be willing to let it lull him back to sleep. He was clearly too stubborn to actually rest, like he should.

"Did I give you anything else?" he asked gruffly, trying to remain polite.

Rory turned his eyes to look pointedly at his wife, who reluctantly extracted the vaguely familiar cylindrical object from her purse. The man made to snatch it away, but Amy kept it just out of his reach.

"Tell me," she said business-like. "Is this a sonic screwdriver?"

The man paused, his grievance slipping away as it occurred to him that these two knew a lot more than what they appeared to. He gave a slow nod, eyeing the woman warily.

A brief smile curled the corners of her mouth upward before she quickly quelled the expression. It wasn't time to get her hopes up yet.

"Then do you mind telling me why you have one?"

"Oh for goodness sake!" exclaimed Rory, exasperated that she wouldn't merely ask him the one question they were both dying to know the answer to.

"Shut up, Rory," Amy cut him off impatiently, needing to be thorough with this subtle interrogation. She arched a finely shaped eyebrow at the man. "Well?"

He growled, frustrated with her barely veiled tactics. "I made it. It's not exactly as top-notched as some of my other models, but it serves its purpose all things considering. Why?"

"Because I had a friend once, the Raggedy Man I would call him, that had a sonic screwdriver that looked almost like this the first time we met. And I can't help but wonder . . . are you him?"

This was starting to get out of hand. "Am I _who_?" he impatiently demanded, having had enough of this.

"Are you the Doctor?"

His expression became slack at the question and it took him a moment to process it. It had been a couple of decades since he had been addressed that way, so to be called such was a bit disconcerting; more alarming was the fact that the two seemed to know who he was—or a version of him rather. It made them knowing what the sonic was much more sense.

"I haven't been called that in years," he remarked with a derisive snort. "I didn't think I'd miss it . . ."

His indirect admittance was enough for Amy to draw closer, concern written across her beaming features. "What happened to you, Doctor?" she asked, gesturing to his prosthetic in particular.

"Just because I missed being called that, doesn't mean I want to!" he snapped, not about to be acknowledged as his original counterpart. To this day it still hurt.

"Then what _are_ we supposed to call you?" asked Rory, trying to remain even-tempered with a man who had evidently already lost what little patience he possessed.

He sank back into the pillows propping him up, struggling to ignore the exhaustion that was fighting to pull him under. He gave a despairing sigh, feeling his options steadily dwindle until there was only one left. While he may pride himself in being stubborn, he knew that he couldn't do this on his own in his present state. He needed to trust them and they, in turn, had to trust him.

It would be no easy feat.

"John," he murmured, all previous ire extinguished from his voice. "My name is John Tyler now. But, while I may be the Doctor, I am not _your _Doctor."

"How do you mean?" inquired Rory, brow furrowed in confusion.

"It's a long story," John admitted. "One that I'll tell you in due time, I assure you, but right now I need your help."

"Anything, Doctor—I mean John," insisted Amy, ready to help this man in any way she could. While it was true, he was not her Doctor, he was still _the_ Doctor; she could see it in his eyes if she looked past all the anger that clouded the surface.

"I need you to bring me back to my TARDIS."

"I don't think that's such a good idea . . ." Rory said as he looked to John uncertainly. It wouldn't be wise to move so soon after surgery. And given the surgical practices and lesser technology of the era, it was likely he wouldn't be allowed out of bed for weeks with the injuries he'd sustained. It was simply out of the question.

But John wasn't about to be told no.

"_Please_ . . ." he implored with a hint of desperation stressing his tone. "You don't understand! I need to get back to my TARDIS right this instant."

"John . . ."

In a surprising display of energy, John strained forward and seized Rory by the collar of his vest, yanking him close as he brought his face near his. He stared with the flare of defiance in his dark eyes as he said, "You'd do anything to save the woman you loved, even if it meant ripping yourself to pieces in the process, wouldn't you? Move heaven and earth just to get her back? Please, if you understand that at all, then please, _please_, help me."

Rory gaped at John for a handful of seconds while the man's words sank in. He'd do anything in a heartbeat if it meant saving Amy; he'd proven so on multiple occasions. And it appeared that this man, who was still somehow the Doctor, was more than willing to prove the same.

The nurse's face settled to a solemn look of mutual understanding as he, against better judgment, agreed.

* * *

Their little, low key adventure hadn't quite turned out as planned. But that, of course, was to be expected.

"You just had to go and insult her, didn't you?!" yelled Clara as she ran behind the Doctor, struggling to keep up with his longer strides.

"How was I supposed to know that making eye contact with her was sacrilegious?" sputtered the Doctor flabbergasted, chancing a quick glance over his shoulder.

Yep, they were still being chased by a horde of angry worshippers wielding torches and crude spears.

"Maybe it would've helped if you, I don't know, noticed that practically everyone was looking at the ground!" she retorted shrilly. "And here I thought you were observant."

"Well, pardon me for merely being polite—or at least attempting to be!"

Any further chastisement was abruptly cut off when a lone spear passed them both, clearing Clara but coming within a hair's breadth of cutting the Doctor's left ear clean off. This prompted the pair to pick up their already stringent pace; weaving through tight corners of the various vendors stalls set up in the populated bazaar in an effort to shake off their pursuers.

They made it breathless to the TARDIS just as another spear was sent their way, clambering over themselves in their haste to get inside and close the door.

The Doctor wasted no time inputting the coordinates back to 21st century Earth, collapsing into the jump seat once they made it safely into the void. He gave a breathless laugh of disbelief as it occurred to him that they had been very close to being burnt at the stake. And it had been quite exciting, maybe even a little fantastic. This chaotic life in which he led was most certainly guaranteed of never getting dull if he found himself fleeing from an angry mob every once in a while.

In a way, it was sort of humbling.

His laughter was contagious and soon Clara was giggling along with him, the slow ebb of adrenaline leaving her quivering from her still slightly shaken nerves.

"I think we've had enough running for the day," chuckled the Doctor, grinning goofily at Clara. "What do you say we take a quick break and have a nice, hot cup of tea before we sail onward into our next adventure?"

"Sounds—" Clara was suddenly interrupted by the jarring motion of the TARDIS making an abrupt landing, shaking her occupants with her many tremors as she settled down.

Once the tremors had seized, the Doctor and Clara looked to each other questioningly, hoping to see that the other had already derived some kind of answer as to what had just happened. When they both proved to be as dumbfounded as the other, the two immediately set off over to the door, stepping out and cautiously looking about.

Nothing seemed out of the ordinary at first glance. They seemed to have appeared at their attended destination—if the scenery was anything to go by. Perhaps they were off by a few years. It was hard to tell without checking the date.

"What do you suppose that was all about?" asked Clara.

"I don't know . . ." said the Doctor carefully. He continued surveying their surroundings pensively.

Why had the TARDIS decided to drop them off with that amount of fanfare? Was something supposed to happen here that she wanted them to see?

"Doctor . . ." Clara began with a sort of trepidation in her voice.

His gaze snapped back to her, concern overtaking his features as he asked, "Yes, what is it?"

Clara gave no further response, her silence proving to be answer enough. He followed her wide-eyed stare, his two hearts nearly stopping when his gaze fell upon the unexpected sight of Clara.

Only it wasn't the Clara Oswald that he knew. It was one of her echoes.

This Clara was in a frightful state. Her hair was greasy and appeared to have been hacked at mercilessly until all that remained was a shaggy, uneven mop. Her clothes were frayed in several places, stained by sweat and dirt and blood. Oh so much blood.

The injuries though, he was astounded that she was even conscious. Her wrists were torn and chaffed, with bruises running up her forearms. At her middle was a sizable tear in her grey shirt that she kept covered with one of her hands, likely concealing a nasty wound. Her face contained various sized scrapes and welts, not a trace of hope remaining in her bloodshot eyes.

She looked so very defeated.

"I've come to deliver a message to the Doctor," she droned on, staring dead-eyed at him.

"That . . . that would be me," he answered warily.

The other Clara gave a slight sigh, a brief flicker of relief shooting across her expression before returning back to the blank mask it had been in previously.

"Silence will fall when the question is asked."

* * *

_Author's Note: We're shifting gears next chapter. I hope that won't bother/upset anyone because it's going to seem like we're backpedaling in terms of moving the plot further. But while that may be the case, the next chapter is by no means a filler. Like I mentioned from the start, things are going to appear out of order in this story with multiple timelines occurring sometimes at the same time like we've seen in the previous chapters._

_If it's not coherent now, trust me that by the end it will be._

_Fun fact: This was meant to be chapter four, while what is now chapter four was meant to be chapter three. I changed my mind about three-quarters of the way of writing both chapters (sometimes I'll simultaneously write two consecutive chapters at the same time if I get stuck at a part in one of them)._

_Next chapter: The Lonely Creature_


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